---
title: "Patrycja_data_wrangling"
author: "Semra Smajic"
date: "11/4/2021"
output: html_document
---
## Load the packages
```{r}
library(plyr)
#library(readr)
library(tidyverse)
#library(stringr)
library(dplyr)
#library(ggplot2)
#library(ggpubr)
#library(Hmisc)
#library(reshape2)
```

## Load the data file. Please make sure of the correct separator in your file (sep = ",")
```{r}
dataset <- read.csv("Z:/Projects/CAMeSyn/Mulica et al., 2023, Assessing the suitability of iPSC-derived human astrocytes/0. Figures and the corresponding data/Fig. 2 - Revised/new/GFAP_VIM_Palm_allrep.csv", header = TRUE, sep = ","); 

dataset <- dataset %>% rename(Well = 1)

```


## Basic operations on columns - data calculation
# This is creating a new column (MyNewResult) with new data that you will calculate
```{r}
dataset$NormalizedmeanDeepRedInCellMask <- dataset$meanDeepRedInCellMask/dataset$NucArea;

dataset$NormalizedmeanGreenInCellMask <- dataset$meanGreenInCellMask/dataset$NucArea;

write.csv(dataset, "C:/Users/semra.smajic/Desktop/MySavedDataset.csv")  # Always rename your .csv file

```


## Data grouping and analysis
# https://bookdown.org/manishpatwal/bookdown-demo/basic-operations-in-r.html
# var - variance
# sd- standard deviation
# mean - mean
# sum - summary
```{r}
analyzed_dataset <- dataset %>% 
  #group_by(Well, Field) %>%    # two levels of grouping
  group_by(Well) %>%        # one level of grouping
  summarise(meanDeepRedInCellMask_mean = (mean(meanDeepRedInCellMask, na.rm = TRUE)),
            meanGreenInCellMask_mean = (mean(meanGreenInCellMask, na.rm = TRUE)),
            NormalizedDeepRedInCellMask_mean = (mean(NormalizedmeanDeepRedInCellMask, na.rm = TRUE)),
            NormalizedGreenInCellMask_mean = (mean(NormalizedmeanGreenInCellMask, na.rm = TRUE))
            )
write.csv(analyzed_dataset, "Z:/Projects/CAMeSyn/Mulica et al., 2023, Assessing the suitability of iPSC-derived human astrocytes/0. Figures and the corresponding data/Fig. 2 - Revised/new/Summary_GFAP_VIM_Palm_allrep.csv")    # Always rename your .csv file

```